A script for updating dom0 and TemplateVMs. Can be run as a cron job.

qubes-update.sh

#!/bin/bash
# Set the updatevm.
updatevm=sys-firewall
# Declare arrays of VMs to be updated.
Fedora=(
'fedora-23'
'fedora-23-minimal'
)
Debian=(
'whonix-gw'
'whonix-ws'
)
# Proceed only if the UpdateVM is running.
if qvm-ls $updatevm | grep -q Running; then
    echo "Starting update process."
    # Download dom0 updates.
    echo "Downloading updates for dom0 at $(date -Is) ...";
    sudo qubes-dom0-update -y;
    sleep 5;
    # Download Fedora VM updates.
    for vm in ${Fedora[*]}; do
        if qvm-ls $vm | grep -q Halted; then
            echo "Updating $vm at $(date -Is) ...";
            qvm-start --no-guid -q $vm;
            sleep 3;
            qvm-run -a --nogui -p -u root $vm 'dnf -y --refresh upgrade';
            sleep 10;
            qvm-shutdown -q --wait $vm;
            sleep 3;
        fi
    done
    #Download Debian VM updates.
    for vm in ${Debian[*]}; do
        if qvm-ls $vm | grep -q Halted; then
            echo "Updating $vm at $(date -Is) ...";
            qvm-start --no-guid -q $vm;
            sleep 3;
            qvm-run -a --nogui -p -u root $vm 'apt-get -y update && apt-get -y dist-upgrade';
            sleep 10;
            qvm-shutdown -q --wait $vm;
            sleep 3;
        fi
    done
    echo "Finished update process at $(date -Is).";
fi
exit